Resources
DATABASES
GENOME ENGINEERING
Addgene
CRISPOR
CRISPR-ID Detecting CRISPR mediated indels by Sanger sequencing
CrispyCrunch a tool for defining batches of CRISPR edits and analyzing their basic effects
ChopChop
CRISP Design
genome-engineering.org
IDT Integrated DNA Technologies
IDT Resuspension Calculator
inDelphi predicts the heterogeneous mixture of indels resulting from microhomology-mediated end-joining (MMEJ) and non-homologous end-joining (NHEJ) at a CRISPR-induced cut.
UNDIAGNOSED AND RARE DISORDERS
Genetic and Rare Diseases Information Center (GARD) of the NCATS, NIH
Rare Diseases Clinical Research Network (RDCRN) of the NCATS, NIH
The portal for rare diseases and orphan drugs (ORPHA)
Undiagnosed Diseases Network (UDN) Harvard
Rare Genomics Institute
ClinGen Explore the clinical relevance of genes & variants
ClinVar aggregates information about genomic variation and its relationship to human health.
GENETIC INFORMATION SERVERS, DATABASES, SEQUENCE ANALYSIS TOOLS
Allen Brain Atlas
Bioconductor
BioGPS
BiQ Analyzer (Visualization and quality control of DNA methylation data from bisulfite sequencing)
BiSearch (Primer-design algorithm for bisulfite converted DNA sequences)
Bowtie (Ultrafast, memory-efficient short read aligner)
Brain Atlas (KEGG)
CpG Plot Search
Database for Annotation, Visualization and Integrated Discovery v6.7
Ensembl
GeneCards (Database of human genes that provides genomic information on known and predicted human genes)
Genetics Home Reference
Gene Expression Omnibus (Public functional genomics data repository)
Gene Ontology
Gene Nomenclature Committee (HUGO)
GTExPORTAL (The Genotype-Tissue Expression (GTEx) project)
Integrative Genomics Viewer (IGV) (High-performance genomics data visualization and exploration)
In-Silico PCR (UCSC)
International Gene Trap Consortium
KEGG Pathway Database (Diagrams of molecular interactions, reactions, and relations)
Livestock Genomics (Provides access to interactive genome maps of cattle and sheep)
MethLAB (Package for the analysis of array-based DNA methylation data)
MethPrimer (Design primers for methylation PCRs)
microRNA predictive models
Mouse Genome Informatics (International database resource for the laboratory mouse)
NEBcutter V2.0 (Find the sites for all Type II and Type III restriction enzymes)
PubMed
Reactome
R environment for statistical computing
RTPrimerDB (Helmholtz Zentrum Munchen Database for primer and probe sequences used in real-time PCR assays)
Sigenae (Information System for Analysis of Breeding Animals’ Genome)
QUMA (Align, visualize and quantify bisulfite sequence data for CpG methylation analysis)
UCSC Genome Bioinformatics (Exploring sequences)
UCSC (Data files formats)
UniGene (View of the transcriptome)
RECOMMENDED
NETWORKS
DATASETS
NextGene
Novel calcineurin A (PPP3CA) mutation in NPCs and NGN2 neurons of patient with epileptic encephalopathy and dysmorphy. Lisowski P, Ploski R. NCBI SRA accession: SRP128828 Temporary Submission ID: SUB3434765
Interferon induced SLFNs and tumorigenesis. Arslan AD, Lisowski P, Platanias LC. NCBI Bioproject PRJNA341338
Adipose tissue mesenchymal stem cells (AMSCs) DNA methylation profile – Illumina NextSeq 500; TruSeq DNA Methylation-seq (RRBS): to be published
HMGN1 and HMGN2 KO in the modulation of cortical and hippocampal transcription – Illumina GAIIx TruSeqmRNA-seq differential exone usage level: to be published
HMGN1 overexpression in the modulation of cortical and hippocampal transcription – Illumina GAIIx TruSeq mRNA-seq differential exone usage level: to be published
MICROARRAYS
Regulatory role of SLFN5 in type I interferon signaling: Arslan AD, Lisowski P, Platanias LC. GEO accession: GSE88771
Essential role of SIRTs in type I interferon signaling: Mehrota S, Lisowski P, Platanias LC. GEO accession: GSE66033
Central role of ULK1 in type I interferon signaling. Saleiro D, Lisowski P, Platanias LC. GEO accession: GSE60778
Transcriptomic analysis of prefrontal cortex, hippocampus, and nucleus accumbens of alcohol preferring and non-preferring rats. Stankiewicz AM, Goscik J, Dyr W, Murat M, Juszczak GR, Ryglewicz D, Swiergiel AH, Wieczorek M, Stefanski R, Lisowski P. GEO accesssion: GSE65064
Gene expression profiling of prefrontal cortex of mice subjected to acute and chronic social stress. Stankiewicz AM, Goscik J, Swiergiel AH, Majewska A, Wieczorek M, Juszczak GR, Lisowski P. GEO accession: GSE64734
Effect of acute and chronic social stress on hippocampal transcriptome in mice. Stankiewicz AM, Goscik J, Gruba K, Majewska A, Swiergiel AH, Juszczak GR, Lisowski P. GEO accession: GSE59070
Effects of chronic desipramine treatment on hippocampal transcriptome in mice differing in response to antidepressants. Lisowski P, Goscik J, Swiergiel AH. GEO accession: GSE27532
Comparing gene expression profiles in the mammary glands of high- and low-milk-yield Holstein Friesian cows. Lisowski P, Goscik J, Kosciuczuk EM, Olbromski R, Bagnicka E, Zwierzchowski L. GEO accesion: GSE33680
Gene expression profiling in bovine mammary gland pathophysiology. Lisowski P, Kosciuczuk E. Goscik J, Jarczak J, Zwierchowski L, Bagnicka E. GEO accession: GSE34031